File __init__.py has 273 lines of code (exceeds 250 allowed). Consider refactoring.

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#!/usr/bin/env python3
# -*- coding: utf-8 -*-
# Copyright 2013-2023 by Björn Johansson.  All rights reserved.
# This code is part of the Python-dna distribution and governed by its
# license.  Please see the LICENSE.txt file that should have been included

Function gelplot_imshow has 20 arguments (exceeds 4 allowed). Consider refactoring.

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def gelplot_imshow(

Function run has 20 arguments (exceeds 4 allowed). Consider refactoring.

Open

    def run(

Function tm_dbd has 19 arguments (exceeds 4 allowed). Consider refactoring.

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def tm_dbd(

Function _all_simple_paths_graph has a Cognitive Complexity of 17 (exceeds 5 allowed). Consider refactoring.

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def _all_simple_paths_graph(G, source, target, cutoff=None):
    if source not in G:
        raise _nx.NetworkXError("source node %s not in graph" % source)
    if target not in G:
        raise _nx.NetworkXError("target node %s not in graph" % source)

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Function T4 has a Cognitive Complexity of 17 (exceeds 5 allowed). Consider refactoring.

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    def T4(self, nucleotides=None):
        """Fill in five prime protruding ends and chewing back
        three prime protruding ends by a DNA polymerase providing both
        5'-3' DNA polymerase activity and 3'-5' nuclease acitivty
        (such as T4 DNA polymerase). This can be done in presence of any

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Function __init__ has a Cognitive Complexity of 17 (exceeds 5 allowed). Consider refactoring.

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    def __init__(
        self,
        record,
        *args,
        # linear=None,

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Function gelplot_imshow has 54 lines of code (exceeds 25 allowed). Consider refactoring.

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def gelplot_imshow(
    distances,
    bandwidths,
    intensities,
    lanes,

Function run has 54 lines of code (exceeds 25 allowed). Consider refactoring.

Open

    def run(
        self,
        field=5.0,  # V/cm
        temperature=295.15,  # K
        runtime=None,  # seconds

File tm.py has 255 lines of code (exceeds 250 allowed). Consider refactoring.

Open

#!/usr/bin/env python3
# -*- coding: utf-8 -*-
# Copyright 2013-2023 by Björn Johansson.  All rights reserved.
# This code is part of the Python-dna distribution and governed by its
# license.  Please see the LICENSE.txt file that should have been included

Function write has a Cognitive Complexity of 16 (exceeds 5 allowed). Consider refactoring.

Open

    def write(self, filename=None, f="gb"):
        """Writes the Dseqrecord to a file using the format f, which must
        be a format supported by Biopython SeqIO for writing [#]_. Default
        is "gb" which is short for Genbank. Note that Biopython SeqIO reads
        more formats than it writes.

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Function shift_location has a Cognitive Complexity of 16 (exceeds 5 allowed). Consider refactoring.

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def shift_location(original_location, shift, lim):
    """docstring."""
    newparts = []
    strand = original_location.strand

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Function toJSON has a Cognitive Complexity of 15 (exceeds 5 allowed). Consider refactoring.

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def toJSON(gbkstring):
    parsed = multipleGB.parseString(gbkstring)

    jseqlist = []

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Function download_text has a Cognitive Complexity of 15 (exceeds 5 allowed). Consider refactoring.

Open

def download_text(url):
    cached = False
    refresh = False
    cache = _shelve.open(
        _os.path.join(_os.environ["pydna_data_dir"], "web"),

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Function synced has a Cognitive Complexity of 15 (exceeds 5 allowed). Consider refactoring.

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    def synced(self, ref, limit=25):
        """This method returns a new circular sequence (Dseqrecord object), which has been rotated
        in such a way that there is maximum overlap between the sequence and
        ref, which may be a string, Biopython Seq, SeqRecord object or
        another Dseqrecord object.

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Function __init__ has a Cognitive Complexity of 14 (exceeds 5 allowed). Consider refactoring.

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    def __init__(self, frags=None, limit=25, algorithm=common_sub_strings):
        # Fragments is a string subclass with some extra properties
        # The order of the fragments has significance
        fragments = []
        for f in frags:

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Function assign_quantitiesB has a Cognitive Complexity of 14 (exceeds 5 allowed). Consider refactoring.

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def assign_quantitiesB(samples, maxdef=Q_(150, "ng")):
    """
    Assigns quantities (masses in nanograms) to the DNA fragments without
    corresponding quantity assuming a linear relationship between the DNA
    length (in basepairs) and its mass. As if the fragments originated in

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Function __getitem__ has a Cognitive Complexity of 13 (exceeds 5 allowed). Consider refactoring.

Open

    def __getitem__(self, i):
        """Save indices of accessed items."""
        if isinstance(i, slice):
            result = self.__class__(self.data[i])
            for ind in range(i.start, i.stop, i.step or 1):

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Function __getitem__ has a Cognitive Complexity of 13 (exceeds 5 allowed). Consider refactoring.

Open

    def __getitem__(self, sl):
        """docstring."""
        answer = Dseqrecord(_copy.copy(self))
        answer.seq = self.seq.__getitem__(sl)
        # answer.seq.alphabet = self.seq.alphabet

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Function ferguson_to_mu0 has a Cognitive Complexity of 13 (exceeds 5 allowed). Consider refactoring.

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def ferguson_to_mu0(
    field,
    Tvals,
    DNAvals,
    dataset,

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